<PAGE>

                                                                    EXHIBIT 10.3

                   SECOND AMENDMENT TO STOCKHOLDER AGREEMENT

         This Second Amendment (the "Second Amendment") to the Stockholder
Agreement dated July 25, 2000 (together with the First Amendment thereto, the
"Stockholder Agreement"), by and among Genencor International, Inc. ("Company"),
Eastman Chemical Company (together with its applicable affiliates "Eastman"),
and Danisco A/S (together with its applicable affiliates "Danisco") is dated the
15th day of November, 2002 and the provisions of this Second Amendment shall be
effective as of the date set forth herein.

                                    RECITALS

         The Parties may desire to expand the total members of directors on the
Board of Directors of the Company without otherwise disturbing the rights of the
Parties currently enjoyed under the Stockholder Agreement. Therefore, the
Parties have agreed to enter into this Second Amendment to achieve the foregoing
objectives.

                                   AGREEMENT

         NOW THEREFORE, in consideration of the premises and covenants set forth
in this Second Amendment and the Stockholder Agreement, the receipt and
sufficiency of which are hereby acknowledged, the Parties hereto agree to amend
the Stockholder Agreement as follows:

1.       The text of Sections 4.1 and 4.3 of the Stockholder Agreement shall be
         deleted in their entirety and replaced by the following text:

                  4.1      Board Composition. The Stockholders and the Company
                           shall take all actions necessary to cause the Board
                           of Directors to be comprised of eleven (11) members,
                           three of whom shall be designees of Eastman (the
                           "Eastman Designees"), three of whom shall be
                           designees of Danisco (the "Danisco Designees," and
                           together with the Eastman Designees, the "Stockholder
                           Designees"), one of whom shall be the Chief Executive
                           Officer of the Company (the "CEO"), one of whom shall
                           be the last persons who are not otherwise affiliates
                           (as defined under the Securities Act and the
                           regulations thereunder) of the Company, Eastman or
                           Danisco (the "Independent Directors").

                  4.3      Voting and Other Actions. The Company and the
                           Stockholder agree to take such actions as are
                           necessary to effectuate the provisions of Sections
                           4.1 and 4.2 both with respect to the time period
                           specified in the first sentence of Section 4.1 and
                           all subsequent elections and appointments of members
                           of the Board. Without limiting the foregoing, the
                           authorized number of members of the Board of
                           Directors shall be no greater than 11 without a
                           further amendment of this agreement in accordance
                           with the provisions of this Agreement. In addition
                           the Company and Stockholders shall also take such
                           other

<PAGE>

                           action as is necessary to ensure that the composition
                           of the Board of Directors is in compliance with the
                           requirements of the Nasdaq National Market.

2.       Except as expressly amended hereby, the provisions of the Stockholder
         Agreement remain unchanged and in full force and effect and this Second
         Amendment does not and shall not be deemed to waive, modify or amend
         any other provision or terms of the Stockholder Agreement.

         IN WITNESS WHEREOF, the Parties' authorized representatives have
executed this Second Amendment as of the day and year first above written.


<TABLE>
<CAPTION>
<S>                                                           <C>
GENENCOR INTERNATIONAL, INC.

By: /s/ Stuart L. Melton
    --------------------------

Its: Senior Vice President
     -------------------------

EASTMAN CHEMICAL COMPANY                                         DANISCO A/S
(On behalf of itself                                             (On behalf of itself and its affiliates)
and its affiliates)

By: /s/ James P. Rogers                                          By: /s/ Alf Duch-Pedersen     /s/ Soren Bjerre-Nielsen
    --------------------------                                       --------------------------------------------------

Its: Chief Financial Officer                                     Its: CEO                      CEO
     -------------------------                                       --------------------------------------------------
</TABLE>